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Genetic analysis of transcription factors in dopaminergic neuronal development in Parkinson’s disease

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Chinese Medical Journal 2024年第4期137卷 450-456页

作者： Yuwen Zhao lixia Qin Hongxu Pan Tingwei Song Yige Wang Xiaoxia Zhou Yaqin Xiang jinchen li Zhenhua liu Qiying Sun Jifeng Guo Xinxiang Yan Beisha Tang Qian Xu Department of Neurology Xiangya HospitalCentral South UniversityChangshaHunan 410008China Department of Neurology The Second Xiangya HospitalCentral South UniversityChangshaHunan 410011China Bioinformatics Center National Clinical Research Center for Geriatric Disorders Xiangya HospitalCentral South UniversityChangshaHunan 410008China Department of Geriatrics Xiangya HospitalCentral South UniversityChangshaHunan 410008China Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics School of Life SciencesCentral South UniversityChangshaHunan 410008China Key Laboratory of Hunan Province in Neurodegenerative Disorders Central South UniversityChangshaHunan 410008China

Background:Genetic variants of dopaminergic transcription factor-encoding genes are suggested to be Parkinson’s disease(PD)risk factors;however,no comprehensive analyses of these genes in patients with PD have been undertaken.Therefore,we aimed to genetically analyze 16 dopaminergic transcription factor genes in Chinese patients with PD.Methods:Whole-exome sequencing(WES)was performed using a Chinese cohort comprising 1917 unrelated patients with familial or sporadic early-onset PD and 1652 controls.Additionally,whole-genome sequencing(WGS)was performed using another Chinese cohort comprising 1962 unrelated patients with sporadic late-onset PD and 1279 controls.Results:We detected 308 rare and 208 rare protein-altering variants in the WES and WGS cohorts,respectively.Gene-based association analyses of rare variants suggested that MSX1 is enriched in sporadic late-onset PD.However,the significance did not pass the Bonferroni correction.Meanwhile,72 and 1730 common variants were found in the WES and WGS cohorts,respectively.Unfortunately,single-variant logistic association analyses did not identify significant associations between common variants and PD.Conclusions:Variants of 16 typical dopaminergic transcription factors might not be major genetic risk factors for PD in Chinese patients.However,we highlight the complexity of PD and the need for extensive research elucidating its etiology.

关键词： Parkinson’s disease Transcription factors Dopaminergic neurons Genetic Variants

HCRVD: A Vulnerability Detection System Based on CST-PDG Hierarchical Code Representation Learning

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Computers, Materials & Continua 2024年第6期79卷 4573-4601页

作者： Zhihui Song jinchen Xu Kewei li Zheng Shan School of Cyberspace Security Information Engineering UniversityZhengzhou450001China

Prior studies have demonstrated that deep learning-based approaches can enhance the performance of source code vulnerability detection by training neural networks to learn vulnerability patterns in code representations.However,due to limitations in code representation and neural network design,the validity and practicality of the model still need to be improved.Additionally,due to differences in programming languages,most methods lack cross-language detection generality.To address these issues,in this paper,we analyze the shortcomings of previous code representations and neural networks.We propose a novel hierarchical code representation that combines Concrete Syntax Trees(CST)with Program Dependence Graphs(PDG).Furthermore,we introduce a Tree-Graph-Gated-Attention(TGGA)network based on gated recurrent units and attention mechanisms to build a Hierarchical Code Representation learning-based Vulnerability Detection(HCRVD)system.This system enables cross-language vulnerability detection at the function-level.The experiments show that HCRVD surpasses many competitors in vulnerability detection capabilities.It benefits from the hierarchical code representation learning method,and outperforms baseline in cross-language vulnerability detection by 9.772%and 11.819%in the C/C++and Java datasets,respectively.Moreover,HCRVD has certain ability to detect vulnerabilities in unknown programming languages and is useful in real open-source projects.HCRVD shows good validity,generality and practicality.

关键词： Vulnerability detection deep learning CST-PDG code representation tree-graph-gated-attention network cross-language

Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-coding Variants

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Genomics, Proteomics & Bioinformatics 2023年第3期21卷 649-661页

作者： Zheng Wang Guihu Zhao Bin li Zhenghuan Fang Qian Chen Xiaomeng Wang Tengfei Luo Yijing Wang Qiao Zhou Kuokuo li Lu Xia Yi Zhang Xun Zhou Hongxu Pan Yuwen Zhao Yige Wang lin Wang Jifeng Guo Beisha Tang Kun Xia jinchen li National Clinical Research Centre for Geriatric Disorders Department of GeriatricsXiangya HospitalCentral South UniversityChangsha 410008China Department of Neurology Xiangya HospitalCentral South UniversityChangsha 410008China Centre for Medical Genetics&Hunan Key Laboratory of Medical Genetics School of Life SciencesCentral South UniversityChangsha 410008China Reproductive Medicine Center Xiangya HospitalCentral South UniversityChangsha 410008China

Non-coding variants in the human genome significantly influence human traits and complex diseases via their regulation and modification effects.Hence,an increasing number of computational methods are developed to predict the effects of variants in human non-coding sequences.However,it is difficult for inexperienced users to select appropriate computational methods from dozens of available methods.To solve this issue,we assessed 12 performance metrics of 24 methods on four independent non-coding variant benchmark datasets:(1)rare germline variants from clinical relevant sequence variants(ClinVar),(2)rare somatic variants from Catalogue Of Somatic Mutations In Cancer(COSMIC),(3)common regulatory variants from curated expression quantitative trait locus(eQTL)data,and(4)disease-associated common variants from curated genomewide association studies(GWAS).All 24 tested methods performed differently under various conditions,indicating varying strengths and weaknesses under different scenarios.Importantly,the performance of existing methods was acceptable for rare germline variants from ClinVar with the area under the receiver operating characteristic curve(AUROC)of 0.4481–0.8033 and poor for rare somatic variants from COSMIC(AUROC=0.4984–0.7131),common regulatory variants from curated eQTL data(AUROC=0.4837–0.6472),and disease-associated common variants from curated GWAS(AUROC=0.4766–0.5188).We also compared the prediction performance of 24 methods for non-coding de novo mutations in autism spectrum disorder,and found that the combined annotation-dependent depletion(CADD)and context-dependent tolerance score(CDTS)methods showed better performance.Summarily,we assessed the performance of 24 computational methods under diverse scenarios,providing preliminary advice for proper tool selection and guiding the development of new techniques in interpreting non-coding variants.

关键词： Non-coding variant Pathogenicity estimation Functional prediction Performance assessment Prediction model

Mapping of de novo mutations in primary biliary cholangitis to a disease-specific co-expression network underlying homeostasis and metabolism

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Journal of Genetics and Genomics 2022年第2期49卷 145-154页

作者： Lu Wang jinchen li Chan Wang Ruqi Tang Jialong liang Yuhua Gong Yaping Dai Ningling Ding Jian Wu Na Dai Lei liu Yi Zhao Youlin Shao Weifeng Zhao Peng Jiang Xingjuan Shi Weichang Chen Ye Tian Xiangdong liu Xiong Ma Zhongsheng Sun Key Laboratory of Developmental Genes and Human Diseases Institute of Life SciencesSoutheast University2 Sipailou RoadNanjingJiangsu 210096China Beijing Institutes of life Science Chinese Academy of SciencesNo.1 West Beichen RoadChaoyang DistrictBeijing 100101China Department of Gastroenterology and Hepatology Shanghai Institute of Digestive DiseasesShanghai Jiao Tong University School of Medicine Afﬁliated Renji Hospital145 Shandong Middle RoadShanghai 200001China Department of Laboratory Medicine The Third People’s Hospital of Zhenjiang300 DaijiamenZhenjiangJiangsu 212021China Department of Laboratory Medicine The Fifth People’s Hospital of Wuxi1215 Guangrui RoadWuxiJiangsu 214000China Department of Hepatology The Fifth People’s Hospital of SuzhouSoochow University10 Guangqian RoadSuzhouJiangsu 215131China Department of Rheumatology First Afﬁliated Hospital of Soochow University188 Shizi RoadSuzhouJiangsu 215006China Department of Gastroenterology Jiangsu University Afﬁliated Kunshan Hospital91 Qianjin West RoadKunshanJiangsu 215300China Department of Gastroenterology Yixing People’s Hospital75 Tongzhenguan RoadYixinJiangsu 214200China Department of Gastrointestinal Endoscopy Eastern Hepatobiliary Surgery Hospital700 Moyu North RoadShanghai 201800China Department of Hepatology The Third People’s Hospital of Changzhou300 Lanling North RoadChangzhouJiangsu 213001China Department of Infectious Diseases First Afﬁliated Hospital of Soochow University188 Shizi RoadSuzhouJiangsu 215006China Department of Gastroenterology First Afﬁliated Hospital of Soochow University188 Shizi RoadSuzhouJiangsu 215006China Department of Radiology Second Afﬁliated Hospital of Soochow University1055 Sanxiang RoadSuzhouJiangsu 215004China Institute of Genomic Medicine Wenzhou Medical UniversityUniversity TownChashanWenzhouZhejiang 325035China

Primary biliary cholangitis(PBC) is an autoimmune disease involving dysregulation of a broad array of homeostatic and metabolic processes. Although considerable single-nucleotide polymorphisms have been unveiled, a large fraction of risk factors remains enigmatic. Candidate genes with rare mutations that tend to confer more deleterious effects need to be identified. To help pinpoint cellular and developmental mechanisms beyond common noncoding variants, we integrate whole exome sequencing with integrative network analysis to investigate genes harboring de novo mutations. Prominent convergence has been revealed on a network of disease-specific co-expression comprised of 55 genes associated with homeostasis and metabolism. The transcription factor gene MEF2 D and the DNA repair gene PARP2 are highlighted as hub genes and identified to be up-and down-regulated, respectively, in peripheral blood data set. Enrichment analysis demonstrates that altered expression of MEF2 D and PARP2 may trigger a series of molecular and cellular processes with pivotal roles in PBC pathophysiology. Our study identifies genes with de novo mutations in PBC and suggests that a subset of genes in homeostasis and metabolism tend to act in synergy through converging on co-expression network, providing novel insights into the etiology of PBC and expanding the pool of molecular candidates for discovering clinically actionable biomarkers.

关键词： Primary biliary cholangitis de novo mutations Whole exome sequencing Transcriptional networks Co-expression

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游戏化在适老产品设计中的应用研究

装饰 2024年第1期 133-135页

作者：蒋金辰陶小惠李玉玲四川美术学院

本文探索了一种基于游戏化的适老产品设计模型,以老年康复类产品为例,探索适老化产品设计方法和路径。文中运用游戏化的交互式设计三要素(使用游戏元素、制定规则边界与积累经验数据),提出提升老年人康复、健身质量的游戏化设计方法。... 详细信息

本文探索了一种基于游戏化的适老产品设计模型,以老年康复类产品为例,探索适老化产品设计方法和路径。文中运用游戏化的交互式设计三要素(使用游戏元素、制定规则边界与积累经验数据),提出提升老年人康复、健身质量的游戏化设计方法。通过数例康复类产品设计初步验证了基于游戏化的适老产品设计模型的可行性。

关键词：游戏化适老产品设计老年人康复健身

Targeted sequencing and integrative analysis of 3,195 Chinese patients with neurodevelopmental disorders prioritized 26 novel candidate genes

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Journal of Genetics and Genomics 2021年第4期48卷 312-323页

作者： Tao Wang Yi Zhang liqui liu Yan Wang Huiqian Chen Tianda Fan jinchen li Kun Xia Zhongsheng Sun Center for Medical Genetics&Hunan Key Laboratory of Medical Genetics School of Life SciencesCentral South UniversityChangshaHunan 410083China Beijing Institutes of life Science Chinese Academy of SciencesBeijing 100101China DIAGenes Precision Medicine Beijing 102600China National Clinical Research Centre for Geriatric Disorders Department of GeriatricsXiangya HospitalCentral South UniversityChangshaHunan 410083China Shanghai Adeptus Biotechnology Shanghai 200126China Institute of Genomic Medicine Wenzhou Medical UniversityWenzhouZhejiang 325035China Department of Neurology Xiangya HospitalCentral South UniversityChangsha Hunan410083China CAS Center for Excellence in Brain Science and Intelligences Technology(CEBSIT) Shanghai 200031China School of Basic Medical Science Central South UniversityChangshaHunan410083China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China State Key Laboratory of Integrated Management of Pest Insects and Rodents Chinese Academy of SciencesBeijing 100101China

Neurodevelopmental disorders(NDDs)are a set of complex disorders characterized by diverse and cooccurring clinical symptoms.The genetic contribution in patients with NDDs remains largely unknown.Here,we sequence 519 NDD-related genes in 3,195 Chinese probands with neurodevelopmental phenotypes and identify 2,522 putative functional mutations consisting of 137 de novo mutations(DNMs)in 86 genes and 2,385 rare inherited mutations(RIMs)with 22 X-linked hemizygotes in 13 genes,2 homozygous mutations in 2 genes and 23 compound heterozygous mutations in 10 genes.Furthermore,the DNMs of16,807 probands with NDDs are retrieved from public datasets and combine in an integrated analysis with the mutation data of our Chinese NDD probands by taking 3,582 in-house controls of Chinese origin as background.We prioritize 26 novel candidate genes.Notably,six of these genes d ITSN1,UBR3,CADM1,RYR3,FLNA,and PLXNA3 d preferably contribute to autism spectrum disorders(ASDs),as demonstrated by high co-expression and/or interaction with ASD genes confirmed via rescue experiments in a mouse model.Importantly,these genes are differentially expressed in the ASD cortex in a significant manner and involved in ASD-associated networks.Together,our study expands the genetic spectrum of Chinese NDDs,further facilitating both basic and translational research.

关键词： De novo mutations X-linked variants Rare inherited variants Homozygous mutations Neurodevelopmental disorders Autism spectrum disorders Candidate genes

粤港澳大湾区内地城市群路网韧性的贝叶斯网络评估

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安全与环境学报 2024年第3期24卷 825-835页

作者：赵荣国杨锦琛李洁周苏华湘潭大学工程结构动力学与可靠性分析湖南省普通高等学校重点实验室湖南湘潭411105 湘潭大学机械工程与力学学院湖南湘潭411105 湘潭大学土木工程学院湖南湘潭411105 湖南大学土木工程学院长沙410083 湖南大学建筑安全与节能教育部重点实验室长沙410083

随着我国城市化进程的推进,城市路网的韧性问题愈发凸显。构建了一种基于贝叶斯网络模型的城市路网韧性评价模型,并以粤港澳大湾区内地城市群为例,评估了2000—2019年该地区9个城市的路网韧性。基于韧性功能函数从容灾性、稳定性、重构... 详细信息

随着我国城市化进程的推进,城市路网的韧性问题愈发凸显。构建了一种基于贝叶斯网络模型的城市路网韧性评价模型,并以粤港澳大湾区内地城市群为例,评估了2000—2019年该地区9个城市的路网韧性。基于韧性功能函数从容灾性、稳定性、重构性、恢复性4个方面建立功能层,选取稳定性、可变性、可维护性、可靠性、服务性、安全性、鲁棒性、可修性、适应性9个因素建立性能层,选取客运量、公共汽车数量、道路面积率、出租车数量、交通事故死亡人数、公共交通投资、每万人公共汽车数、道路运输从业人数、人均道路面积9个因素建立因素层。研究结果表明:路网韧性指数最高的为深圳(60%),而最低的为中山(43%);广州、深圳、珠海、东莞的路网韧性一直稳定增长,其余城市的路网韧性浮动较小;路网韧性并非总是随着城市GDP的增长而提高,还与人均GDP有关;敏感性分析表明,路网重构性、路网可靠性、交通事故死亡人数分别为各自所在层中对路网韧性影响最大的因素;加强中心城市与其他城市之间的联系可以提高城市路网韧性。研究成果可为粤港澳大湾区城市群交通路网功能完善与韧性提升提供技术参考。

关键词：安全系统学韧性评价贝叶斯网络敏感性分析粤港澳大湾区地理信息系统

2型糖尿病患者峰值摄氧量与临床资料的相关性研究

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黑龙江医学 2024年第4期48卷 395-398页

作者：白金晨李英天津市天津医院康复科天津300211 天津市第三中心医院内分泌科天津300170

目的:探究2型糖尿病(type 2 diabetes mellitus,T2DM)患者峰值摄氧量与临床资料的相关性。方法:选取2019年3月—2022年3月天津市第三中心医院收治的138例T2DM患者作为研究对象,探究心肺运动试验(cardiopulmonary exercise test,CPET)检... 详细信息

目的:探究2型糖尿病(type 2 diabetes mellitus,T2DM)患者峰值摄氧量与临床资料的相关性。方法:选取2019年3月—2022年3月天津市第三中心医院收治的138例T2DM患者作为研究对象,探究心肺运动试验(cardiopulmonary exercise test,CPET)检测的峰值摄氧量与临床资料的相关性。相关系数用r表示,0<|r|≤0.3提示相关性较弱,0.3<|r|≤0.7提示相关性中等,0.7<|r|≤1提示相关性较强。采用多元线性回归分析方法分析T2DM患者峰值摄氧量的独立影响因素。结果:T2DM患者的峰值摄氧量与体质量指数(BMI)、腰围、T2DM病程呈弱负相关,差异有统计学意义(r=-0.214、-0.250、-0.230,P<0.05),与男性和HDL-C呈弱正相关,差异有统计学意义(r=0.120、0.220,P<0.05),与握力/体质量呈中等强度正相关,差异有统计学意义(r=0.389,P<0.05),与左心室舒张功能障碍(LVDD)呈中等强度负相关,差异有统计学意义(r=-0.321,P<0.05)。多元线性回归分析结果显示,LVDD、腰围是T2DM患者峰值摄氧量的独立危险因素,握力/体质量、男性性别是T2DM患者峰值摄氧量的独立保护因素。结论:LVDD、腰围是T2DM患者峰值摄氧量的独立危险因素,握力/体质量、男性是T2DM患者峰值摄氧量的独立保护因素,T2DM患者握力/体质量降低会增加心肺耐力受损的发生风险。本研究提供了一种简单、方便的预测T2DM患者心肺耐力受损的方法,并为预防及治疗T2DM患者心肺耐力受损提供了理论依据。

关键词： 2型糖尿病握力/体质量峰值摄氧量独立影响因子

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中国芦笋出口外销形势分析

农业展望 2024年第3期20卷 102-108页

作者：孙芳杨锦琛李丹常德市农业农村局湖南常德415000 长沙马王堆农产品股份有限公司湖南长沙410133 湖南省农业信息与工程研究所湖南长沙410125

芦笋是中国出口市场的重要农产品之一,目前中国芦笋产业已发展成为具有竞争优势的新兴产业,在全球芦笋贸易中占有举足轻重的地位。本研究基于联合国粮食及农业组织(FAO)和中国海关的中国芦笋出口数据,分析了近10年中国芦笋的出口变化特... 详细信息

芦笋是中国出口市场的重要农产品之一,目前中国芦笋产业已发展成为具有竞争优势的新兴产业,在全球芦笋贸易中占有举足轻重的地位。本研究基于联合国粮食及农业组织(FAO)和中国海关的中国芦笋出口数据,分析了近10年中国芦笋的出口变化特征。结果表明:中国芦笋出口以鲜或冷藏芦笋、芦笋罐头为主,鲜或冷藏芦笋主要满足国内消费和销往邻近的中国地区和亚洲发达国家,以广东、湖南、云南、江苏、福建5省生产为主;芦笋罐头是中国出口创汇的主力军,主要由福建、山东、安徽、山西4个省份生产,销往西班牙、德国、荷兰、法国和丹麦等欧盟市场。近几年受发达国家贸易壁垒、新冠疫情等因素影响,中国芦笋出口呈现明显下降趋势。根据对中国芦笋出口形势的分析结果,推动中国芦笋产业高质量发展,需提高芦笋精深加工技术、增加产品附加值,规模化发展、打造芦笋产业集群,积极应对贸易壁垒、提高芦笋国际市场竞争力,实施有机认证和标准化战略、提高芦笋质量安全标准,实施多元化战略、进一步拓宽芦笋出口市场。最后,对未来中国芦笋出口前景进行了展望。

关键词：鲜或冷藏芦笋芦笋罐头出口量出口额